There’s a view that politics and national security should be oil and water–that some iron rule of Washington should make the two impossible to mix. In reality, it doesn’t work that way. Even so, Susan Rice’s removal of her name from consideration to be Barack Obama’s next Secretary of State is what happens when the fallout from a genuine national security disaster runs headlong into the electrified domestic politics of an election year.

It’s hard to know whether the United Nations Ambassador truly reached this conclusion on her own, or whether she accepted the White House’s view that, with the nation’s fiscal future in the balance, this is no time for an ugly confirmation fight with Republicans. But Rice was surely correct when she said, in a public letter to the president, that “the confirmation process would be lengthy, disruptive and costly” to the president’s priorities. “The tradeoff,” she added, “is simply not worth it to our country.”

Either way, Obama must see this as an unusually bitter political defeat. He is personally close to Rice, who led his 2008 campaign foreign policy team, and whom he had previously defended with a certain gusto. (“If [Republicans] want to go after somebody, they should go after me,” he growled last month.) Obama was also said to believe that a president is entitled to choose his foreign policy–a view many liberals invoked when they grudgingly confirmed another woman named Rice as Secretary of State seven years ago.

It’s hard to believe that Rice’s chief Republican opponents, who include Senators John McCain and Lindsey Graham, really think she was complicit in a political cover-up of the true nature of the September 11 attacks in Benghazi that claimed the life of four Americans. The ostensible case against Rice rested on the strange idea that, in several television appearances on September 15, she should not have repeated information vetted for public consumption by the intelligence community. This is a particularly odd complaint at a time when conservatives are up in arms over alleged national security leaks from this White House.

The Republicans’ motives are impossible to know. But other theories for their intense opposition to Rice are at least as persuasive. One is that Rice’s chief tormenter, John McCain, carries both a personal disdain for her (Rice was a withering critic of McCain’s foreign policy in 2008) and a kinship with his fellow Vietnam War veteran, John Kerry, who is currently assumed to be a shoo-in for the job. Kerry’s nomination would also, perhaps not incidentally, give the recently-ousted GOP Senator Scott Brown a chance to reclaim his seat, reducing the Democrats’ Senate majority by one. Another is that Rice was a lightning rod for lingering Republican anger over the Benghazi tragedy in general. Although Rice’s statements, inaccurate as they were, were reasonable for the still-confused moment at which she made them, the White House’s public commentary, including some of Obama’s own statements, did take a curiously long and meandering path to the truth at a time when Mitt Romney was trying to use Benghazi as a battering ram against Obama’s record on terrorism. It might not have been “the biggest cover up in history”; it might not have been a cover-up at all. (There’s no evidence that it was.)

But many Republicans remain convinced that, in the heat of a campaign, politics influenced the White House’s response and have not gotten over it. “When it comes to Benghazi I am determined to find out what happened — before, during and after the attack,” Graham said in a statement after Rice’s withdrawal. “Unfortunately, the White House and other agencies are stonewalling when it comes to providing the relevant information. I find this unacceptable.”

Some think Rice could have survived the assault over her Benghazi comments–but not more recent criticism on other fronts–including her investment portfolio and her record on Africa dating back to the 1990s. Critics were also painting a portrait of Rice–one her allies call unfair and even sexist–as brusque and undiplomatic. (Compounding her woes was a recent tour of Capitol Hill that only seemed to make her predicament worse.) One Capitol Hill source with close ties to Obama’s foreign policy team recently told TIME he thought these additional issues might be the decisive factor in preventing her from succeeding the soon-to-depart Hillary Clinton as America’s top diplomat.

There may yet be a happy ending for Rice, who is reportedly eager to leave her New York-based assignment and return to her family in Washington. Obama is said to be considering making Rice his next national security advisor–a position with less prestige but far more influence over foreign policy than Secretary of State–and one that doesn’t require the approval of cranky senators. The hitch is that Obama’s current national security advisor, Tom Donilon, is happy in his job–and while he might happily leave it for Clinton’s job, he could face his own confirmationheadaches.

But if a solution can be found, Rice’s critics may wind up regretting this fight. Back when Obama was preparing to take office in 2008, he made it known he wanted the intelligence community insider John Brennan to run his CIA. Outraged liberals shot down the pick, arguing (probably inaccurately) that Brennan had been complicit in harsh Bush-era detention and interrogation policies. So instead, Obama installed Brennan in a West Wing office steps away from his own, as his counter terrorism advisor. Brennan is now among the administration’s most powerful figures, largely directing the global campaign against terrorism. If Republicans genuinely believe that Susan Rice can’t be trusted to handle national security, they may wind up wishing that she had become a diplomat abroad, not a policymaker in the West Wing.